Suberin--a biopolyester forming apoplastic plant interfaces

Suberized cell walls form physiologically important plant-environment interfaces because they act as barriers that limit water and nutrient transport and protect plants from invasion by pathogens. Plants respond to environmental stimuli by modifying the degree of suberization in root cell walls. Salt stress or drought-induced suberization leads to a decrease in radial water transport in roots. Although reinforced, suberized cell walls never act as absolutely impermeable barriers. Deeper insights into the structure and biosynthesis of suberin are required to elucidate what determines the barrier properties. Progress has been obtained from analytical methods that enabled the structural characterization of oligomeric building blocks in suberin, and from the opening of suberin research to molecular genetic approaches by the elucidation of the chemical composition and tissue distribution of suberin in the model species Arabidopsis.     

Dynamic exploration and editing of KEGG pathway diagrams

MOTIVATION: The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database is a very valuable information resource for researchers in the fields of life sciences. It contains metabolic and regulatory processes in the form of wiring diagrams, which can be used for browsing and information retrieval as well as a base for modeling and simulation. Thus it helps in understanding biological processes and higher-order functions of biological systems. Currently the KEGG website uses semi-static visualizations for the presentation and navigation of its pathway information. While this visualization style offers a good pathway presentation and navigation, it does not provide some of the possibilities related to dynamic visualizations, most importantly, the creation and visualization of user-specific pathways. RESULTS: This paper presents methods for the dynamic visualization, interactive navigation and editing of KEGG pathway diagrams. These diagrams, given as KEGG Markup Language (KGML) files, can be visually explored using novel approaches combining semi-static and dynamic visualization, but also edited or even newly created and then exported into KGML files. AVAILABILITY: KGML-ED, a program implementing the presented methods, is available free of charge to the scientific community at http://kgml-ed.ipk-gatersleben.de.     

Calcium from LactoCalcium milk mineral after digestion with pepsin stimulates mineralized bone nodule formation in human osteoblast-like SaOS-2 cells in vitro and may be rendered bioavailable in vivo

Many individuals cannot obtain the optimum calcium requirement from food for a variety of reasons. Therefore, calcium supplements are important sources of dietary calcium. One of the calcium sources commercially available is LactoCalcium (milk minerals) that has 28% calcium, and a 2:1 ratio of calcium to phosphorus. The objectives of this study were (a) to examine whether calcium can be released from LactoCalcium by using digestive enzymes and (b) to determine its biological activity by examining its ability to stimulate bone formation. LactoCalcium was treated in vitro by using simulated gastric and intestinal fluids or porcine gastric, pancreatic and intestinal extracts. Our results indicate the role of enzymes or bile extract in the digestion of the product. We show that, by increasing the concentration of pepsin at a fixed concentration of LactoCalcium (substrate), the percentage of released calcium increased in a dose-dependent manner, showing that, at the right enzyme concentration, as much as 100% of the calcium present in LactoCalcium can be made available. The biological activity of the digested calcium was demonstrated by the stimulation of mineralized bone nodules in SaOS-2 cells in a dose-dependent manner. Thus, 1 mM and 3 mM calcium released from LactoCalcium increased the nodule area by 23.17 mm(2) (p<0.0001) and 77.78 mm(2) (p<0.0001), respectively, as compared to a value of 0.99 mm(2) at 0.5 mM calcium from LactoCalcium. These results demonstrate the in vitro bioavailability and bioactivity of calcium from LactoCalcium and serve as a basis for carrying out in vivo analyses to determine the suitability of using LactoCalcium as a source of calcium for individuals at risk of developing osteoporosis.     

Degradation of polycyclic aromatic hydrocarbons in soil by a two-step sequential treatment

The objectives of this work were to isolate the microorganisms responsible for a previously observed degradation of polycyclic aromatic hydrocarbons (PAH) in soil and to test a method for cleaning a PAH-contaminated soil. An efficient PAH degrader was isolated from an agricultural soil and designated as Mycobacterium LP1. In liquid culture, it degraded phenanthrene (58%), pyrene (24%), anthracene (21%) and benzo(a)pyrene (10%) present in mixture (initial concentration 50 μg ml⁻¹ each) and phenanthrene (92%) and pyrene (94%) as sole carbon sources after 14 days of incubation at 30°C. In soil, Mycobacterium LP1 mineralised ¹⁴C-phenanthrene (45%) and ¹⁴C-pyrene (65%) after 10 days. The good ability of this Mycobacterium was combined with the benzo(a)pyrene oxidation effect obtained by 1% w/w rapeseed oil in a sequential treatment of a PAH-spiked soil (total PAH concentration 200 mg kg⁻¹). The first step was incubation with the bacterium for 12 days and the second step was the addition of the rapeseed oil after this time and a further incubation of 22 days. Phenanthrene (99%), pyrene (95%) and anthracene (99%) were mainly degraded in the first 12 days and a total of 85% of benzo(a)pyrene was transformed during the whole process. The feasibility of the method is discussed.     

Fungal rDNA signatures in coronary atherosclerotic plaques

Bacterial DNA has been found in coronary plaques and it has therefore been concluded that bacteria may play a role as trigger factors in the chronic inflammatory process underlying coronary atherosclerosis. However, the microbial spectrum is complex and it is not known whether microorganisms other than bacteria are involved in coronary disease. Fungal 18S rDNA signatures were systematically investigated in atherosclerotic tissue obtained through catheter-based atherectomy of 38 patients and controls (unaffected coronary arteries) using clone libraries, denaturating gradient gel analysis (DGGE), in situ hybridization and fluorescence in situ hybridization (FISH). Fungal DNA was found in 35 of 38 (92.11%) coronary heart disease patients by either polymerase chain reaction (PCR) with universal primers or in situ hybridization analysis (n = 5), but not in any control sample. In a clone library with more than 350 sequenced clones from pooled patient DNA, an overall richness of 19 different fungal phylotypes could be observed. Fungal profiles of coronary heart disease patients obtained by DGGE analysis showed a median richness of fungal species of 5 (range from 2 to 9) with a high interindividual variability (mean similarity 18.83%). For the first time, the presence of fungal components in atherosclerotic plaques has been demonstrated. Coronary atheromatous plaques harbour diverse and variable fungal communities suggesting a polymicrobial contribution to the chronic inflammatory aetiology.     

Anoctamin-6 Controls Bone Mineralization by Activating the Calcium Transporter NCX1

Anoctamin-6 (Ano6, TMEM16F) belongs to a family of putative Ca²⁺-activated Cl⁻ channels and operates as membrane phospholipid scramblase. Deletion of Ano6 leads to reduced skeleton size, skeletal deformities, and mineralization defects in mice. However, it remains entirely unclear how a lack of Ano6 leads to a delay in bone mineralization by osteoblasts. The Na⁺/Ca²⁺ exchanger NCX1 was found to interact with Ano6 in a two-hybrid split-ubiquitin screen. Using human osteoblasts and osteoblasts from Ano6^−/− and WT mice, we demonstrate that NCX1 requires Ano6 to efficiently translocate Ca²⁺ out of osteoblasts into the calcifying bone matrix. Ca²⁺-activated anion currents are missing in primary osteoblasts isolated from Ano6 null mice. Our findings demonstrate the importance of NCX1 for bone mineralization and explain why deletion of an ion channel leads to the observed mineralization defect: Ano6 Cl⁻ currents are probably required to operate as a Cl⁻ bypass channel, thereby compensating net Na⁺ charge movement by NCX1.     

Adeno-Associated Virus Type 2 Rep68 Can Bind to Consensus Rep-Binding Sites on the Herpes Simplex Virus 1 Genome

Adeno-associated virus type 2 is known to inhibit replication of herpes simplex virus 1 (HSV-1). This activity has been linked to the helicase- and DNA-binding domains of the Rep68/Rep78 proteins. Here, we show that Rep68 can bind to consensus Rep-binding sites on the HSV-1 genome and that the Rep helicase activity can inhibit replication of any DNA if binding is facilitated. Therefore, we hypothesize that inhibition of HSV-1 replication involves direct binding of Rep68/Rep78 to the HSV-1 genome.